A year ago, when she was in kindergarten in Fountain, Colo., Coy Mathis became a girl. Until that point, Coy — born a boy — had resisted the boyish t-shirts and jeans that her parents laid out for her, hated the boy’s backpack she had to carry to school. She wanted to wear tutus and princess dresses, to grow her hair long, to slip into pink Mary Janes.

“I am a girl,” she told her parents starting at age 3. After visits to a pediatrician and a psychologist who advised her parents, as mom Kathryn Mathis puts it, “to let her live as who she was,” they finally did. Three months after kindergarten began, Coy transitioned from being a boy to living as a girl.

Kindergarteners are pretty forgiving folks, so they accepted that Coy now wore dresses with leggings and used the girls’ bathroom. But in December, Coy’s elementary-school principal issued an ultimatum from the school district: Coy could no longer frequent the girls’ bathroom; she would have to head to private bathrooms reserved for teachers or sick children — or enter the boys’ bathroom.

Coy’s parents presented the school with a copy of Colorado’s anti-discrimination law, which protects transgender people’s right to use a bathroom that matches their gender identity. The school didn’t budge, so the Mathis family pulled Coy out to homeschool her and teamed up with the Transgender Legal Defense & Education Fund to file a complaint with the state Division of Civil Rights. The school district has until mid-March to respond.

The unusual case points up the need for schools to discuss whether transgender students may need accommodation — or entirely new policies. Might a boy who identifies as a girl and plays on the school tennis team have an advantage over her teammates? Will transgender girls go out for varsity football?

Sixteen states have laws that prohibit discrimination on the basis of gender identity. But no one tracks how many schools have official policies on how to treat transgender students, says Michael Silverman, executive director of the Fund and one of the Mathis family’s attorneys. “In most situations when school districts are presented with appropriate transgender information, they tend to want to do the right thing,” he says. “We have always been able to resolve the situation.”

Until now. This week, Coy’s school district, Fountain-Fort Carson School District 8, issued a statement that it “firmly believes it has acted reasonably and fairly with respect to this issue” and is preparing a response to the family’s formal complaint. Silverman is hopeful that Coy’s situation will raise awareness of the need for schools to formulate more comprehensive gender-discrimination policies. “It’s an emerging civil rights issue that we’ll need to address,” he says.

Meanwhile, Coy, 6, has become a media darling, flitting from Katie to CNN. It was not her parents’ intention. “We don’t want to put ourselves out there for the kinds of harassment and speculation that come along with media attention but at the same time the school stigmatized her and we really felt we needed to hold them accountable for what they were doing,” says Mathis, 27, a professional photographer and mother of five.

She and her husband have also been confronted with questions about how someone as young as Coy can be sure about her gender identification. But it’s not unheard of for children who are 6 — or younger — to express uneasiness with their gender. Still, it can be difficult to figure out which children are simply testing boundaries or having fun with pretend play — boys clickclacking around in their mothers’ high heels, for example — and which truly feel they’ve been born into the wrong body. “It’s normal for children to want to break out of gender boxes when they’re little,” says Diane Ehrensaft, director of mental health at the Child and Adolescent Gender Center in San Francisco and author of Gender Born, Gender Made. “But transgender children have a need to say, I’m not the person you think I am.”

The best thing parents can do is respect their kids’ gender preferences. “I’m not saying it’s easy to be a transgender child in our culture, but it’s a lot easier than trying to be a boy when you know you’re not,” says Ehrensaft. “Once parents get on board, the children calm down, they are happier, they relax into themselves.”

That’s exactly what happened with Coy. When her parents were forcing her to cut her hair short and shun skirts, she acted depressed and rebellious. “As soon as she switched to her true identity, she started making friends and her grades went up,” says her mother.

At 6, of course, changing gender is as easy as changing clothes. Around age 11, Coy can take medication that blocks puberty. Hormones may be offered at around age 16, along with a visit to a gender specialist to determine if Coy fully understands the implications of undergoing gender-reassignment surgery.

Mathis and her husband have been reading books and canvassing transgender children and adults, asking them how their experience could have been improved in an effort to smooth Coy’s transition. Even after a year, they’re still adjusting to having four girls and a boy instead of three girls and two boys. Says Mathis: “I don’t think anybody ever expects to have a transgender child.”